Lesk: Introduction to Genomics, third edition Chapter 1, Answers for Exercises

Exercise 1.1. 3 × 104 protein-coding genes/3 × 109 bp = 1 protein-coding gene per 105 bp.

Exercise 1.2. (a) density of differences ∼ 1/1500, estimate of total number of differences = 3 × 109 bp/1500
bp/difference = 2 million
(b) total number of differences = 3 × 109 /100 = 30 million

Exercise 1.3. (a) 0.002 × 1000 = 2.

(b) fraction of protein-coding sequence = 0.011 = fraction of sequence differences in protein-coding regions

Exercise 1.4. (a) 210 = 1024 (b) 220 ∼ 1 million (c) 220 ∼ 1 million (d) 3/220

Exercise 1.5. 25000 genes × 300 amino acids/gene × 3 bases/amino acid = 22500000 bases. Multiplying by a
factor of 2 for control regions gives an estimate of 45 Mb.

Exercise 1.6. (a) many possibilities: UUU and UUC both code for phenylalanine. (b) UUA and CUA both code
for leucine. (c) AUA codes for Ile, AUG codes for Met (d) not for codons that encode amino acids; UAA and
UGA are both STOP codons. (e) UUU → UAU. (f) AGU → CGU. (g) 3. (h) CGG. (i) (1) Phe → Ser, Tyr,
Cys, Leu, Ile, Val. (2) Ser → all except Met, Val, His, Gln, Lys, Asp, Glu

Exercise 1.7. Ser → Phe, Ser → Leu, Pro → Leu, Thr → Ile, Thr → Met, Ala → Val

Exercise 1.8. It would in many cases (but of course not all) be tolerable. Even helical regions in RNA can
accomodate deletions by ‘looping out’ of the unmatched base.

Exercise 1.9. mitochondrial DNA from individuals in Gibraltar share haplotypes with both source populations.

Exercise 1.10. This is in part a trick question. I am not aware of any species of kangaroo that shows alleles for
different coat colours as cats do. If not, that’s the answer. If there were such a species, there is no guarantee
that the gene is on the X chromosome. If not, that’s the answer. But if there were a species of kangaroo that
had a locus on the X chromosome with alleles for different coat colours, then still there could be no calico
kangaroos because marsupial females inactivate the same X chromosome in all cells.

Exercise 1.11. (a) No, the gene produces a functional protein in infancy. (b) Not on the X chromosome.

Exercise 1.12. It might predispose the patient to antisocial behaviour.

Exercise 1.13. The orange individual at the upper left, sharing haplotype M16 with individuals with haplotypes
represented by green and purple, probably came from Algeria.

Exercise 1.14. p13.3 and q22.1

c Arthur M. Lesk 2017 1

Lesk: Introduction to Genomics, third edition Chapter 1, Answers for Exercises

Exercise 1.15. (a) See green asterisk in accompanying figure.

(b) 7 genes/(175000 - 130000) bp = 0.00016 genes/bp

(c) The regions are:

5′ −UTR bases 1–134 aggccg . . . cccacc

Exon 1 bases 135–230 atggtg . . . gagagg
Intron 1 bases 231–347 tgaggc . . . cgcagg
Exon 2 bases 348–551 atgttc . . . ttcaag
Intron 2 bases 552–691 gtgagc . . . gcacag
Exon 3 bases 692–820 ctccta . . . cgttaa
3′ −UTR bases 821–1138 gctgga . . . agtggc

c Arthur M. Lesk 2017 2

Lesk: Introduction to Genomics, third edition Chapter 1, Answers for Exercises

Exercise 1.16.
Exon 1: MVLSPADKTNVKAAWGKVGAHAGEYGAEALER
Exon 2: MFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVA
HVDDMPNALSALSDLHAHKLRVDPVNFK
Exon 3: LLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR

Exercise 1.17. Extent of inverted repeats shown in upper case:

1 GGGGTCTGAC GCTCAGTGGA ACGAAAACTC ACGTTAAGca acgttttctg cctctgacgc

61 ctcttttaat ggtctcagat gacctttggt caccagttct gccagcgtga aggaataatg

...

4861 tttttaattt aaaaggatct aggtgaagat cctttttgat aatctcatga ccaaaatccC

4921 TTAACGTGAG TTTTCGTTCC ACTGAGCGTC AGACCCC

Exercise 1.18. If only a single small population is left, genome sequencing could identify pair of individuals
with (relatively) dissimilar genome sequences. Breeding these animals would help to maintain the variety of the
gene pool. If a natural population were under threat from a disease, it might be possible to identify sequences
characteristic of resistant individuals, and preferentially breed them.

c Arthur M. Lesk 2017 3